Published in Genome Res on November 07, 2008
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol (2009) 3.58
Structure and activity of putative intronic miRNA promoters. RNA (2010) 2.50
Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol (2010) 1.84
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res (2011) 1.62
A minicircuitry involving REST and CREB controls miR-9-2 expression during human neuronal differentiation. Nucleic Acids Res (2010) 1.58
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet (2011) 1.41
Epigenetic Control of MicroRNA Expression and Aging. Curr Genomics (2009) 1.28
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol (2012) 1.13
RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One (2010) 1.07
Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silence (2010) 1.06
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics (2010) 1.05
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics (2011) 1.04
Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02
Histone deacetylase regulates high mobility group A2-targeting microRNAs in human cord blood-derived multipotent stem cell aging. Cell Mol Life Sci (2010) 1.01
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol (2013) 0.99
Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One (2011) 0.96
Biogenesis of intronic miRNAs located in clusters by independent transcription and alternative splicing. RNA (2013) 0.96
Regulation of microRNA biogenesis and turnover by animals and their viruses. Cell Mol Life Sci (2013) 0.95
Finding associations among histone modifications using sparse partial correlation networks. PLoS Comput Biol (2013) 0.93
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Res (2010) 0.90
MicroRNA regulation of T-lymphocyte immunity: modulation of molecular networks responsible for T-cell activation, differentiation, and development. Crit Rev Immunol (2013) 0.87
Principles of miRNA-target regulation in metazoan models. Int J Mol Sci (2013) 0.86
Epigenetic regulation and functional characterization of microRNA-142 in mesenchymal cells. PLoS One (2013) 0.84
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res (2012) 0.83
High DNA melting temperature predicts transcription start site location in human and mouse. Nucleic Acids Res (2009) 0.83
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. Epigenetics (2010) 0.83
Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis. Front Genet (2014) 0.81
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. Nucleic Acids Res (2014) 0.80
Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Med Genomics (2013) 0.79
microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes. Mol Biol Evol (2016) 0.78
Genomic features and computational identification of human microRNAs under long-range developmental regulation. BMC Genomics (2011) 0.78
SNOntology: Myriads of novel snoRNAs or just a mirage? BMC Genomics (2011) 0.78
A unique histone deacetylase inhibitor alters microRNA expression and signal transduction in chemoresistant ovarian cancer cells. Cancer Biol Ther (2012) 0.78
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species. BMC Genomics (2008) 0.78
Illuminating microRNA Transcription from the Epigenome. Curr Genomics (2013) 0.77
A Double Negative Loop Comprising ETV6/RUNX1 and MIR181A1 Contributes to Differentiation Block in t(12;21)-Positive Acute Lymphoblastic Leukemia. PLoS One (2015) 0.76
Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species. ScientificWorldJournal (2014) 0.76
Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS One (2012) 0.76
Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data. Bayesian Anal (2013) 0.75
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics (2012) 0.75
MicroRNA Promoter Identification in Arabidopsis Using Multiple Histone Markers. Biomed Res Int (2015) 0.75
DNA methylation patterns facilitate the identification of microRNA transcription start sites: a brain-specific study. PLoS One (2013) 0.75
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. BMC Bioinformatics (2010) 0.75
Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability. Genome Med (2017) 0.75
MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Chromatin modifications and their function. Cell (2007) 55.98
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
MicroRNA genes are transcribed by RNA polymerase II. EMBO J (2004) 20.65
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
Identification of mammalian microRNA host genes and transcription units. Genome Res (2004) 14.63
Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell (2007) 14.58
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA (2004) 11.52
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol (2006) 6.81
The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A (2006) 6.09
Computational identification of promoters and first exons in the human genome. Nat Genet (2001) 5.88
Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A (2007) 5.20
Direct regulation of an oncogenic micro-RNA cluster by E2F transcription factors. J Biol Chem (2006) 4.57
Genome-wide approaches to studying chromatin modifications. Nat Rev Genet (2008) 4.28
An evolutionarily conserved mechanism for microRNA-223 expression revealed by microRNA gene profiling. Cell (2007) 3.34
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol (2007) 2.86
Characterization of a highly variable eutherian microRNA gene. RNA (2005) 2.72
The Eukaryotic Promoter Database EPD. Nucleic Acids Res (1998) 2.24
Sequence-dependent DNA structure: tetranucleotide conformational maps. J Mol Biol (2000) 2.13
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics (2002) 1.85
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics (2001) 1.80
Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res (2007) 1.80
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Identification of human gene core promoters in silico. Genome Res (1998) 1.26
Boosting with stumps for predicting transcription start sites. Genome Biol (2007) 1.08
Computational analyses of eukaryotic promoters. BMC Bioinformatics (2007) 0.99
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics (2007) 0.83
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
ZOOM! Zillions of oligos mapped. Bioinformatics (2008) 29.78
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
A microRNA component of the p53 tumour suppressor network. Nature (2007) 19.25
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev (2002) 7.61
Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res (2009) 7.42
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58
A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A (2007) 5.16
Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56
Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc (2009) 4.45
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
Critical roles for Dicer in the female germline. Genes Dev (2007) 4.23
Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
Deregulation of scribble promotes mammary tumorigenesis and reveals a role for cell polarity in carcinoma. Cell (2008) 3.43
Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J (2010) 3.18
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08
Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol (2002) 3.00
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69
A complete sequence of the T. tengcongensis genome. Genome Res (2002) 2.60
Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell (2009) 2.54
MicroRNA identification based on sequence and structure alignment. Bioinformatics (2005) 2.52
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A (2005) 2.36
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12
Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res (2006) 2.00
Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron (2012) 1.85
Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80
Chaperonins facilitate KNOTTED1 cell-to-cell trafficking and stem cell function. Science (2011) 1.73
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res (2005) 1.70
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics (2013) 1.64
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Comparative analysis of amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six eukaryotic genomes. Mol Biol Evol (2003) 1.59
Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metab (2008) 1.55
Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics (2004) 1.54
Neural potential of a stem cell population in the hair follicle. Cell Cycle (2007) 1.53
Conservation of small RNA pathways in platypus. Genome Res (2008) 1.51
Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci (2014) 1.51
RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A (2008) 1.45
Development of the human cancer microRNA network. Silence (2010) 1.43
Poly A- transcripts expressed in HeLa cells. PLoS One (2008) 1.42
SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (2011) 1.42
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res (2013) 1.41
Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol (2007) 1.41
Statistical significance of cis-regulatory modules. BMC Bioinformatics (2007) 1.41
Functional genomics as applied to mapping transcription regulatory networks. Curr Opin Microbiol (2002) 1.39
Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics (2006) 1.39
Predicting methylation status of CpG islands in the human brain. Bioinformatics (2006) 1.38
Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem (2008) 1.38
Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol (2004) 1.35
Computing exact P-values for DNA motifs. Bioinformatics (2007) 1.33
Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics (2008) 1.31
H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc Natl Acad Sci U S A (2012) 1.28
Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One (2011) 1.25
Finding anchors for genomic sequence comparison. J Comput Biol (2005) 1.25
The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity (2013) 1.23
Estrogen receptor beta binds to and regulates three distinct classes of target genes. J Biol Chem (2010) 1.21
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res (2006) 1.21
Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mamm Genome (2006) 1.21
A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis. Elife (2013) 1.20
Stomatin-like protein 2 is overexpressed in cancer and involved in regulating cell growth and cell adhesion in human esophageal squamous cell carcinoma. Clin Cancer Res (2006) 1.19
Epistatic module detection for case-control studies: a Bayesian model with a Gibbs sampling strategy. PLoS Genet (2009) 1.17
CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPAR delta/beta-mediated adaptation to metabolic stress. J Biol Chem (2008) 1.16
DWE: discriminating word enumerator. Bioinformatics (2004) 1.15
DNA methylation data analysis and its application to cancer research. Epigenomics (2013) 1.14
Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PLoS Genet (2011) 1.14
Scanning the human genome at kilobase resolution. Genome Res (2008) 1.13
Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc Natl Acad Sci U S A (2007) 1.10